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Yorodumi- PDB-8b2w: Millisecond cryo-trapping by the spitrobot crystal plunger, CTX-M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8b2w | ||||||
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Title | Millisecond cryo-trapping by the spitrobot crystal plunger, CTX-M-14 E166A, Ampicillin, 500 MS | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / beta-lactamase / CTX-M-14 / time-resolved crystallography | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Doepke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. ...Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Doepke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / Tellkamp, F. / Schulz, E.C. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Millisecond cryo-trapping by the spitrobot crystal plunger simplifies time-resolved crystallography. Authors: Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Dopke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / ...Authors: Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Dopke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / Tellkamp, F. / Schulz, E.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b2w.cif.gz | 142.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b2w.ent.gz | 91.5 KB | Display | PDB format |
PDBx/mmJSON format | 8b2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8b2w_validation.pdf.gz | 826.4 KB | Display | wwPDB validaton report |
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Full document | 8b2w_full_validation.pdf.gz | 828.5 KB | Display | |
Data in XML | 8b2w_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 8b2w_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/8b2w ftp://data.pdbj.org/pub/pdb/validation_reports/b2/8b2w | HTTPS FTP |
-Related structure data
Related structure data | 8aw8C 8aw9C 8awbC 8awcC 8awdC 8aweC 8awfC 8awsC 8awuC 8awvC 8awxC 8awyC 8b03C 8b05C 8b06C 8b08C 8b2oC 8b2vC 8b3mC 6gthS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27600.119 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ctx-m-14 / Production host: Escherichia coli (E. coli) / References: UniProt: D2D9A0, beta-lactamase |
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#2: Chemical | ChemComp-AIX / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.23 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 4.5 / Details: 40% PEG8000, 200 mM LiSO4, 100 mM NaOAc, pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97626 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 22, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→77.621 Å / Num. obs: 13533 / % possible obs: 79.9 % / Redundancy: 10.1 % / Biso Wilson estimate: 17.23 Å2 / CC1/2: 0.999 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.78→2.084 Å / Num. unique obs: 677 / CC1/2: 0.714 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6gth Resolution: 1.78→38.81 Å / SU ML: 0.2075 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.4146 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.78→38.81 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 5.76488902473 Å / Origin y: -1.26228966718 Å / Origin z: 19.7022979875 Å
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Refinement TLS group | Selection details: all |